Chromosomal translocations are guided by the spatial organization of the genome

There is little known about how the location of DNA double-strand breaks (DSBs) in the 3D genome influences their translocation potential genome wide. We now employ genome-wide approaches to directly address this question in G1-arrested pro-B cell lines. In these cells, antigenreceptor loci cleaved by RAG endonuclease are dominant partners for I-SceI DSB translocations regardless of genomic position, reflecting the driving force of high frequency DSBs at these loci and their co-localization in a fraction of cells. This dominance of DSB-driven hotspots obviates direct assessment of spatial proximity contributions to translocation formation. Therefore, we normalized genomic DSB frequency via ionizing-radiation. Under these conditions, RAG-induced hotspots were minimized and translocations were highly enriched in cis along the I-SceI breaksite chromosome and within other chromosomes and sub-chromosomal domains in a manner directly related to pre-existing spatial proximity. This influence of 3D genome organization on translocations provides a new lens through which to view genomic aberrations in cancer.